IMO your switch from Comcast to FiOS was smart. Comcast is changing all their systems nationwide to encrypt all channels, which make boxes like the HW or iView useless on their systems. But because of their system design, FiOS doesn't need to encrypt all channels. Also, FiOS rebroadcasts PSIP on the OTA channels they rebroadcast, so on those channels you can use the EPG, timed recordings, etc. Those functions don't work on most other cable systems.
I'm an OTA user but share your frustration with the bugs, especially the second one. Even OTA, this happens to me - a lot. It seems any change to the station's channel map or channel names, no matter how minor, will trigger the HW to reload the whole channel from scratch, in the process losing any Skip or Favorite flags and restoring any deleted subchannels.
In DFW we have one station, K31GL, that's our Retro TV affiliate, and it really confuses the HW. Any change to this station and the HW weirdly loses all subchannels except 31.5 (a useless infomercial channel), and I have to manually scan channel 31 to get Retro back, skip or delete 31.5 again, and re-enter my timers for Retro. It'll be OK for a while, then K31GL will relabel another channel and I have to go through it all over again!
The iView and HW firmware have converged somewhat since the early days. From what I can tell from reports, most of the iView's more serious bugs have been fixed, and iView and HW now pretty much share the same bugs. You can even load iView firmware on a HW or vice versa, although you'll need a remote that matches the firmware you use, and there may be some other incompatibilities. Some folks load HW firmware onto iViews to disable the mostly useless display (but then they have to use the HW remote).
loaded iView firmware onto his HW in order to use the nicer iView remote, and I plan on trying that myself next week.